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Old 03-13-2015, 04:49 AM   #3
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Location: Ottawa, Ontario

Join Date: Sep 2014
Posts: 9

Thanks for the reply Michael. I adjusted the lfc threshold and it certainly made the list a bit more manageable (LFC > 1.5, FDR=0.05 yielded about 800 DEGs in both directions). I guess I just wasn't expecting such large differences between the two conditions and was concerned that I was missing some obvious artefact that could cause it.

I also ran the PCA following regularize log transformation to look at distances. PC1 is apparently capturing 100% variance and splits the two conditions. I'm no expert, so correct me if I'm wrong, but I suppose this supports that idea that the results are just the product of very distinct conditions because the variability between biological replicates is negligible (at least relative to the differences between conditions).

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